Add support to pdbqt datatype

lib/galaxy/datatypes/molecules.py

@@ -492,6 +492,57 @@ def set_peek(self, dataset, is_multi_byte=False):
             dataset.peek = 'file does not exist'
             dataset.blurb = 'file purged from disk'
 
+class PDBQT(GenericMolFile):
+    """
+    PDBQT Autodock and Autodock Vina format
+    http://autodock.scripps.edu/faqs-help/faq/what-is-the-format-of-a-pdbqt-file
+    """
+    file_ext = "pdbqt"
+
+    def sniff(self, filename):
+        """
+        Try to guess if the file is a PDBQT file.
+
+        >>> from galaxy.datatypes.sniff import get_test_fname
+        >>> fname = get_test_fname('NuBBE_1_obabel_3D.pdbqt')
+        >>> PDBQT().sniff(fname)
+        True
+
+        >>> fname = get_test_fname('drugbank_drugs.cml')
+        >>> PDBQT().sniff(fname)
+        False
+        """
+        headers = get_headers(filename, sep=' ', count=300)
+        h = t = c = s = k = e = False
+        for line in headers:
+            section_name = line[0].strip()
+            if section_name == 'COMPND':
+                h = True
+            elif section_name == 'REMARK':
+                t = True
+            elif section_name == 'ROOT':
+                c = True
+            elif section_name == 'ENDROOT':
+                s = True
+            elif section_name == 'BRANCH':
+                k = True
+            elif section_name == 'TORSDOF':
+                e = True
+
+        if h * t * c * s * k * e:
+            return True
+        else:
+            return False
+
+    def set_peek(self, dataset, is_multi_byte=False):
+        if not dataset.dataset.purged:
+            atom_numbers = count_special_lines("^ATOM", dataset.file_name)
+            hetatm_numbers = count_special_lines("^HETATM", dataset.file_name)
+            dataset.peek = get_file_peek(dataset.file_name, is_multi_byte=is_multi_byte)
+            dataset.blurb = "%s atoms and %s HET-atoms" % (atom_numbers, hetatm_numbers)
+        else:
+            dataset.peek = 'file does not exist'
+            dataset.blurb = 'file purged from disk'
 
 class grd(data.Text):
     file_ext = "grd"

lib/galaxy/datatypes/test/NuBBE_1_obabel_3D.pdbqt

@@ -0,0 +1,55 @@
+REMARK  9 active torsions:
+REMARK  status: ('A' for Active; 'I' for Inactive)
+REMARK    1  A    between atoms: C_2  and  O_3 
+REMARK    2  A    between atoms: C_2  and  C_14 
+REMARK    3  A    between atoms: O_3  and  C_4 
+REMARK    4  A    between atoms: C_4  and  C_5 
+REMARK    5  A    between atoms: C_6  and  C_8 
+REMARK    6  A    between atoms: C_8  and  C_9 
+REMARK    7  A    between atoms: C_9  and  C_10 
+REMARK    8  A    between atoms: C_16  and  O_17 
+REMARK    9  A    between atoms: C_19  and  O_20 
+ROOT
+ATOM      1  O   LIG d   1      -0.947  -0.436  -3.210  0.00  0.00    -0.259 OA
+ATOM      2  C   LIG d   1      -1.207   0.245  -2.235  0.00  0.00     0.293 C 
+ENDROOT
+BRANCH   2   3
+ATOM      3  O   LIG d   1      -1.935  -0.114  -1.151  0.00  0.00    -0.314 OA
+BRANCH   3   4
+ATOM      4  C   LIG d   1      -2.338  -1.483  -1.065  0.00  0.00     0.206 C 
+BRANCH   4   5
+ATOM      5  C   LIG d   1      -1.745  -2.032   0.200  0.00  0.00     0.002 C 
+ATOM      6  C   LIG d   1      -0.550  -2.644   0.338  0.00  0.00    -0.085 C 
+ATOM      7  C   LIG d   1       0.405  -2.885  -0.801  0.00  0.00     0.043 C 
+BRANCH   6   8
+ATOM      8  C   LIG d   1      -0.086  -3.153   1.694  0.00  0.00     0.037 C 
+BRANCH   8   9
+ATOM      9  C   LIG d   1       0.730  -2.114   2.473  0.00  0.00     0.031 C 
+BRANCH   9  10
+ATOM     10  C   LIG d   1       1.187  -2.618   3.818  0.00  0.00    -0.024 C 
+ATOM     11  C   LIG d   1       2.352  -3.233   4.110  0.00  0.00    -0.091 C 
+ATOM     12  C   LIG d   1       3.401  -3.605   3.099  0.00  0.00     0.042 C 
+ATOM     13  C   LIG d   1       2.699  -3.614   5.527  0.00  0.00     0.042 C 
+ENDBRANCH   9  10
+ENDBRANCH   8   9
+ENDBRANCH   6   8
+ENDBRANCH   4   5
+ENDBRANCH   3   4
+ENDBRANCH   2   3
+BRANCH   2  14
+ATOM     14  C   LIG d   1      -0.778   1.657  -2.066  0.00  0.00     0.042 A 
+ATOM     15  C   LIG d   1      -0.640   2.224  -0.790  0.00  0.00     0.057 A 
+ATOM     16  C   LIG d   1      -0.249   3.551  -0.677  0.00  0.00     0.099 A 
+ATOM     17  C   LIG d   1       0.012   4.308  -1.816  0.00  0.00     0.098 A 
+ATOM     18  C   LIG d   1      -0.102   3.753  -3.083  0.00  0.00     0.040 A 
+ATOM     19  C   LIG d   1      -0.494   2.419  -3.212  0.00  0.00     0.020 A 
+BRANCH  16  20
+ATOM     20  O   LIG d   1      -0.104   4.159   0.540  0.00  0.00    -0.358 OA
+ATOM     21  HO  LIG d   1       0.164   5.067   0.617  1.00  0.00     0.217 HD
+ENDBRANCH  16  20
+BRANCH  17  22
+ATOM     22  O   LIG d   1       0.389   5.614  -1.691  0.00  0.00    -0.358 OA
+ATOM     23  HO  LIG d   1       0.567   6.131  -2.469  1.00  0.00     0.217 HD
+ENDBRANCH  17  22
+ENDBRANCH   2  14
+TORSDOF 9